Fecal Microbiome Transplant (FMT) For Chronic UTIs

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Dr. Sahil Khanna doesn’t treat UTIs— he is a gastroenterologist at Mayo Clinic in Rochester, Minnesota. However, gut health plays a crucial role in UTI prevention, and the research published by Dr. Khanna and his colleagues suggests new possibilities for chronic UTI patients.

Gut Bacteria Cause UTI

Urinary tract infections are caused by bacteria that normally live in your colon. The bacteria ascend from the anus toward the urethra and, as a result, could cause a UTI.

The worst type of UTIs is caused by multi-drug resistant organisms (MDRO), which are bacteria that have developed resistance to multiple types of antibiotics. As a result, the MDRO superbugs are extremely hard to kill. However, if there is a way to control the population of multi-drug resistant bacteria in your gut, there is a chance to prevent UTIs that are tough to cure, and this is where gastroenterologists could help.

Antibiotics & Gut Flora

Long courses of wide-spectrum antibiotics are a known culprit of imbalanced gut flora that could lead to diarrhea. In some patients, gut flora suffers so much that they develop Clostridium difficile (C. diff) infection.

C. diff infection could cause symptoms ranging from diarrhea to life-threatening inflammation of the colon, and patients are often referred to gastroenterologists for treatment. Despite using strong intravenous antibiotics like Vancomycin for patients with this disease, C. diff recurs in as many as 15-30% of patients after an initial bout, and up to 65% of these patients will have it again after antibiotic therapy is stopped.

The bottom line, it’s not an easy disease to deal with.

“C. diff is an interesting infection caused by antibiotics and treated with antibiotics,” as Dr. Khanna puts it. The use of antibiotics represents a double-edged sword by suppressing both the pathogen as well as the protective microbiota. And not surprisingly, this controversy inspired researchers to look for alternative solutions besides antibiotics.

Restore Gut Flora To Cure Infection

In 2011, an international team of gastroenterologists developed, tested and published a new non-antibiotic treatment protocol for C. diff.  They suggested that an alternative approach “to restore the damaged microbial intestinal communities” might be more effective than introducing new antibiotics that caused the problem in the first place.

Since the 60s, doctors have been experimenting with fecal microbiome transplants (FMT). Simply put, FMT is an enema with feces taken from a healthy individual and administered to a patient with gastroenterological problems. In fact, in veterinary medicine, FMT has been used to treat gastrointestinal disorders in horses for centuries, so the approach predates the invention of antibiotics and has a high success rate.

The repeated and chronic use of antibiotics to treat infection has an adverse effect on the intestinal flora and could encourage the growth of MDRO. However, by introducing healthy flora (in this case, via an enema of donor feces), the “imbalance can be corrected, the cycle interrupted, and normal bowel function re-established,” suggested the paper.

In the past 15 years, FMT became a recognized approach to treat C. diff, even though it is still labeled as an experimental procedure. Under current FDA rules, physicians are allowed to perform FMT if patients are not responding to antibiotic treatment. The Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA) included the FMT procedure in their official guidelines for C. diff treatment in 2018.


Since Dr. Khanna treats many C. diff patients with FMT, his team was able to retrospectively review patients’ charts and find those who–besides struggling with C. diff–also had a history of chronic UTIs. In the selected cohort of patients, all chronic UTIs (3 or more per year) were confirmed with a positive culture and typical symptoms in a year prior to FMT.

After the treatment with FMT, the following results were observed:

  1. A significant decrease in UTI recurrence in patients who were successfully treated with FMT.
  2. After the procedure, the UTI-causing bacteria that had shown resistance in the year prior to FMT demonstrated improved susceptibility to a range of antibiotics. For example, in three cases, E.coli cultured in the urine of these patients was resistant to Ciprofloxacin prior to FMT but became susceptible to that antibiotic after FMT.

“These findings,” concludes the report, “could mean gut decolonization of MDROs or a reduction in the concentration of these organisms below a threshold to cause UTI.”

In terms of method of action, researchers are still unsure why “less virulent opportunistic bacteria replace MDR bacteria,” says Dr. Khannas, but they do now know that this phenomenon is “a process of competitive exclusion and colonization.”

Probiotics vs. FMT

So why not use strong probiotics to restore gut flora instead of an enema with feces? It certainly sounds unpleasant, you may argue. Unfortunately, the use of probiotics for C. diff hasn’t been successful, with several clinical studies arriving at inconclusive results. Though unsure why, Dr. Khanna and his team noted that “bacterial colonies thrive better together,” emphasizing that it’s “not only bacteria that matter, but the bacterial suspension also matters.”

Imagine that you want to plant a tropical flower in your backyard. One method would be to drop a seed in the soil and hope it grows, but another is to transfer the flower, together with a chunk of its original surrounding soil. In this case, you are not only moving the organism itself but a significant part of its native ecosystem, as well.

The same goes for FMT versus probiotic supplements: We know that probiotic supplements are transient and are washed out of our system within days, while the microbiome obtained via FMT successfully colonizes the recipient for years to come.

A Second Opinion

Dr. Benjamine Davido, an infectious disease specialist with Raymond Poincaré hospital (France), is cautiously optimistic about the findings presented by Dr. Khanna’s team. With respect to the decreased number of UTI recurrences after an FMT procedure, he points out that C. diff infection manifests itself as diarrhea which could lead to UTI. One could argue, then, that by curing C. diff, you effectively remove diarrhea as a risk factor for recurrent UTIs.

Dr. Davido also agrees with the researchers that the small sample size and lack of microbiome profiling pre and post-FMT limited the study. He says that if a larger trial size of particular patients—” for example, folks with MDRO UTI”—could be researched, the findings would be more interesting.

“FMT is not a magic bullet. My point of view as an infectious disease specialist is that we need to deal with bacterial resistance and avoid antibiotics or use narrow antibiotics like Monurol (Fosfomycin)… When we address MDRO [with FMT], we are dealing with the top of the pyramid. For UTI, we ill-treat patients to begin with,” concludes Dr. Davido.

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